Hey, come now. The Dark Knight was nowhere as desaturated as Man of Steel. I just saw TDK in IMAX 70mm a few weeks ago, it did have a bleach-bypass look but it didn't have the pasty dishwater colors of MOS. Not by a long shot.
And TDK was shot on film and looks like it was actually photochemically timed. Nolan's color timing, as projected on film in a theater, is worlds away superior to MOS' color.
That said, you are right about MOS. Of all the classic superheroes, Superman NEEDS to have those primary colors. In some scenes his outfit looked almost black, that's how desaturated it got.